init orphan

entrypoint.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+set -euo pipefail
+
+case "${DISABLE_IMPORT:-false}" in
+    false) ;;
+    true|load)
+        echo "DISABLE_IMPORT is ${DISABLE_IMPORT} - skipping ETL pipeline (neo4j handles the rest)"
+        exit 0
+        ;;
+    *)
+        echo "Invalid DISABLE_IMPORT='${DISABLE_IMPORT}' - expected false, true or load" >&2
+        exit 1
+        ;;
+esac
+# Wait for a file to appear, with a timeout so the container can't hang forever.
+# Usage: wait_for_file <path> [timeout_seconds]
+wait_for_file() {
+    local file="$1"
+    local timeout="${2:-300}"
+    local waited=0
+    while [ ! -f "$file" ]; do
+        if [ "$waited" -ge "$timeout" ]; then
+            echo "Timed out after ${timeout}s waiting for $(basename "$file")" >&2
+            exit 1
+        fi
+        echo "Waiting for $(basename "$file")..."
+        sleep 5
+        waited=$((waited + 5))
+    done
+}
+
+# Start from an empty import dir: BioCypher appends new -partNNN files next to
+# old ones and the admin import globs all of them, so leftovers would be
+# imported again. Stale marker files would also break the handshake below.
+echo "Clearing /neo4j_import..."
+find /neo4j_import -mindepth 1 -delete
+
+# Make the import dir accessible to both the Python app and Neo4j
+chmod -R 777 /neo4j_import
+
+#echo "Waiting for Neo4j to be ready..."
+#python wait-for-neo4j.py
+
+echo "Running Python data processing script..."
+#python import_fhir_to_nx_diGraph.py
+python multiple_adapters.py
+
+echo "Running Neo4j import..."
+# Give downstream services a moment before touching the database
+sleep 5
+
+# Wait for the shell script to finish writing its data
+wait_for_file /neo4j_import/shell-scipt-complete
+
+# Signal that data is prepared and ready to import
+touch /neo4j_import/ready-to-import
+chmod 777 /neo4j_import/ready-to-import
+
+# Wait for the import to complete
+echo "Waiting for Neo4j import to complete..."
+wait_for_file /neo4j_import/import-complete
+
+echo "Database setup complete!"